You would know if you had.
Go into the Xposed installer app and uninstall the framework (we can reinstall it later - you wont lose any settings) then reboot. This should rule out anything xposed related. If it's still happening its nothing to do with xposed as it doesnt make changes to actual system files.
But now of course I don't have my xposed frameworks and modules
So I got up and reinstalled the xposed module and on and checked each module..
Apparently the 3 dot menu button on every application kept the navigation bar from going up.
Thanks alot rootSU for your help and guidence!